It would be possible to have a cloud that would merge terms with the same name from different taxonomies. However WordPress doesn’t really have somewhere useful that you could link those tags to, at least not that I know of.

Other people have requested some way to get a specialized rendering of a cloud, some kind of hook where you could customize the markup that gets generated by the plugin. A hook like that could be used to merge terms with the same name together and provide a link relevant to your site, or just remove the link.